Changes to the GEP Web Framework - Fall 2014

Change log for the Genomics Education Partnership Web Framework
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Changes to the GEP Web Framework - Fall 2014

Post by wleung » Sat Aug 23, 2014 6:14 pm

Hello Everyone,

We have reset the GEP Web Framework for the 2014 Fall semester. The list of key changes are summarized below:

1. Annotation and sequence improvement projects for Fall 2014 2. Doodle poll on GEP webinar schedule
  • Doodle Poll (The times listed are in CDT)
  • Please sign up by 7pm CDT next Sunday (08/31/2014)
3. Synchronize GEP annotation resources to FlyBase release 6.01

4. New curriculum for TSS annotation and motif finding 5. Updated curriculum materials
  • Revisions based on FlyBase release 6.01
6. GEP web framework updates
  • GEP UCSC Genome Browser, Gene Record Finder, and the Small Exon Finder
The section below contains a more detailed description of the changes we have made for the 2014 Fall semester:

1. Annotation and sequence improvement projects for Fall 2014

For annotation, we will work on a set of 75 annotation projects from the D. biarmipes Muller D element (Jan. 2014 (GEP/3L Control) assembly) this Fall. In addition to annotating the coding regions, we would also like to ask your students to try to annotate the transcription start sites (TSS) if time permits. The GEP Annotation Report contains a new "Transcription start sites (TSS) report form" section where your students can document the evidence used to support their TSS annotations. Please note that annotating the TSS are optional and you can submit a project without the TSS annotations. Later this Fall, we will also setup projects from the D. biarmipes Muller F element that would only require the annotation of the TSS.

Some sequence motifs are enriched in the region surrounding the TSS in D. melanogaster. Your students can access the list of Drosophila core promoter motifs through the Core Promoter Motifs link on the GEP web site (under "Projects" -> "Annotation Resources"). I have also added two new evidence tracks that highlight each instance of the core promoter motifs on each strand separately (see the Core Promoter Motifs (Plus) and Core Promoter Motifs (Minus) tracks under "Mapping and Sequencing Tracks", respectively).

FlyBase has recently updated the D. melanogaster genome assembly to release 6. This is the first time that the D. melanogaster assembly has changed since 2005. FlyBase has encountered some migration issues (particularly with GBrowse) in early August but these technical issues have now been resolved. We have updated the GEP curriculum and web framework resources to FlyBase release 6.01 for the 2014 Fall semester.

Dr. Elgin and Chris have developed a new protocol (see the Quick Check of Student Annotations document) to quickly check the gene models submitted by your students. We would like to ask you to check the student annotations using this protocol prior to project submission. You can download the protocol through the "GEP Specific Issues" section of the GEP website.

For sequence improvement, we will continue to work on the set of projects from the D. biarmipes Muller F and D elements from last year. Please note that, unlike previous years, your students will need to run the additional PCR and sequencing reactions locally to resolve low quality regions or gaps in the assembly. Alternatively, please add a "dataNeeded" tag to these regions so we can design the primers and run the necessary PCR reactions during Summer 2015.

2. Doodle poll on GEP webinar schedule

We have previously introduced the TSS annotation and motif finding protocols during the alumni workshops this summer. We have revised the walkthroughs and protocols based on the feedback from the alumni workshops. The current versions of the documents are posted on the Beyond Annotation section of the GEP web site.

I plan to host two webinars in early September to provide an overview of the TSS annotation protocol. These webinars will cover the same materials as my alumni workshop presentations this summer. (You can access the alumni workshop presentations through the GEP Private Wiki.)

For those who are interested in attending the webinar, I have setup a Doodle poll to determine the best times for the webinars. Please sign up for the times that would work best for you by 7pm CDT next Sunday (08/31/2014). We will then select the two times that would allow most of the faculty members to attend the webinars. We also plan to record at least one of the webinar sessions so that you can view or download the recordings later.

If you are interested in learning more about the new sequence improvement protocol for the hybrid assemblies, please contact Chris directly to setup an individual consultation session.

3. Synchronize annotation resources to FlyBase release 6.01

The BLASTX report in the annotation packages, databases for the Gene Record Finder and Gene Model Checker, Annotation Files Merger and the BLASTX protein alignment track on the Genome Browser have all been updated to FlyBase release 6.01.

We have also construct a new genome browser for the D. melanogaster release 6 assembly. You can access the new genome browser by selecting the "D. melanogaster" under the "genome" field and "July 2014 (BDGP R6)" under the "assembly" field in the Genome Browser Gateway page.

4. New curriculum for TSS annotation and motif finding
  • Quick Check of Student Annotations
  • Searching for Transcription Start Sites in Drosophila
  • Annotation of Transcription Start Sites in Drosophila
  • Annotation of Conserved Motifs in Drosophila
  • Motif Discovery in Drosophila
5. Updated curriculum materials

We have updated many of the annotation curriculum materials to maintain compatibility with the most recent records in the various databases (e.g. NCBI, FlyBase, and UniProt).

=== Annotation ===
  • Annotation of Drosophila
  • Common Annotation Errors
  • An Introduction to NCBI BLAST
  • Introduction to ab initio and Evidence-based Gene Finding
  • List of Common Bioinformatics Programs
  • Simple Annotation Problem
  • Exercise #1: Detecting and Interpreting Genetic Homology
  • Exercise #2: Using mRNA and EST Evidence in Annotation
  • Chimp BAC Analysis
  • GEP Annotation Report
  • Annotation Strategy Guide
  • Drosophila: Annotation Goals: Final Presentation and Written Reports
=== Sequencing improvement ===
We have moved the sequence improvement materials for the Sanger assemblies to a separate Sanger Sequencing section because they do not apply to the hybrid assemblies. Chris has revised the following curriculum materials for Fall 2014:
  • Using Consed Graphically
  • GEP Hybrid Assembly Walkthrough
  • Sequence Improvement Protocol for GEP Hybrid Assembly Projects
  • PCR Primer Selection Guide
6. GEP web framework updates
  • Genome Browsers for the four genomes paper
    Gene models created by GEP students are available through the "GEP Genes" track (under the "Genes and Gene Prediction Tracks" section)
    • D. melanogaster Apr. 2006 (DBGP R5/dm3) assembly
    • D. erecta Feb. 2006 (CAF1/DereWGS) assembly
    • D. mojavensis Apr. 2014 (GEP/DmojImproved) assembly
    • D. grimshawi Apr. 2014 (GEP/DgriImproved) assembly
  • Gene Record Finder
    • Replaced Y's in the CDS and exon usage map with the exon number in each isoform
    • Change labels in the CDS usage map section to protein names
    • New "Isoforms with unique coding exons" table shows the list of isoforms with identical coding sequences
    • "Download CDS Workbook" creates the Excel workbook in Open XML format (xlsx). Increased the default column width of Excel workbook.
    • Updated "View in GBrowse" link to GBrowse 2 on FlyBase
    • Bug fix for autocomplete search box race condition in Safari
    • Bug fix for CDS usage map layout issues on Google Chrome
  • Small Exon Finder
    • Re-implement the search engine to run the search locally within the web browser to improve search performance
    • Perform iterative search with different CDS sizes if there are no candidates with the target CDS size
    • Bug fix for identifying overlapping small exon candidates
    • Bug fix for finding small exon candidates near search boundaries
    • Thanks to Jim Youngblom and Chris Jones for their bug reports and their ideas on how we can improve the Small Exon Finder

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